Contacts of the helix formed by residues 200 - 208 (chain B) in PDB entry 2R5N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A GLU 5.5 0.4 - - - +
207A ALA* 2.9 23.9 + - - +
198B THR 3.4 2.4 + - - -
199B ASP* 1.3 68.5 - - - +
201B THR* 1.3 58.2 + - - +
202B ALA* 3.5 10.2 + - - +
203B MET* 3.1 45.9 + - + +
204B ARG 2.9 23.7 + - - -
214B ARG* 4.9 3.2 + - - -
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B MET* 3.9 35.7 - - + -
182B TYR* 4.1 15.9 + - + -
197B PHE* 3.8 15.6 - - - -
199B ASP* 3.1 22.4 + - - +
200B ASP* 1.3 72.8 + - - +
202B ALA* 1.3 62.2 + - - +
204B ARG* 3.3 11.1 + - - +
205B PHE* 3.0 31.5 + - + -
240B LEU* 4.2 6.1 - - + -
242B MET* 4.1 11.1 - - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ASP* 3.2 6.6 + - - +
201B THR* 1.3 78.3 - - - +
203B MET* 1.3 56.9 + - - +
205B PHE* 3.2 1.8 + - - -
206B GLU* 2.9 32.7 + - - +
212B VAL* 3.7 23.4 - - + +
214B ARG* 3.5 39.7 - - + +
242B MET* 4.1 14.5 - - + +
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 3.6 27.4 - - + +
206A GLU* 3.9 12.8 - - + +
207A ALA* 3.6 25.1 - - + -
200B ASP* 3.1 35.9 + - + +
202B ALA* 1.3 73.7 - - - +
204B ARG* 1.3 65.4 + - - +
206B GLU* 3.3 6.8 + - - +
207B ALA* 2.9 23.0 + - - +
214B ARG* 3.9 10.4 - - - +
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 3.2 28.8 + - - -
204A ARG* 4.8 6.3 - - + +
207A ALA* 3.5 14.7 - - + +
208A TYR* 4.6 7.9 - - + -
158B MET* 2.9 42.0 + - - +
163B SER* 2.8 28.5 + - - -
164B HIS* 3.2 19.0 - - - +
197B PHE* 5.5 0.2 - - - -
199B ASP* 4.0 11.1 + - - +
200B ASP 2.9 11.5 + - - +
201B THR* 3.4 15.0 + - - +
203B MET* 1.3 76.7 - - - +
205B PHE* 1.3 70.1 + - - +
207B ALA* 3.1 26.2 + - - +
208B TYR* 2.9 38.5 + - + +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B MET* 4.9 3.4 - - + -
158B MET* 3.5 37.2 - - + -
163B SER* 5.4 0.4 - - - -
167B CYS* 3.6 39.5 - - + -
201B THR* 3.0 22.7 + - + +
204B ARG* 1.3 98.7 - - + +
206B GLU* 1.3 65.6 + - - +
208B TYR* 3.0 19.5 + + - +
210B TRP* 3.0 56.0 + + + +
212B VAL* 3.7 18.6 - - + -
240B LEU* 3.6 17.5 - - + -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ASP* 5.5 0.5 - - - +
203A MET* 4.0 15.2 - - + +
202B ALA 2.9 16.3 + - - +
203B MET* 3.7 7.0 - - - +
205B PHE* 1.3 75.0 - - - +
207B ALA* 1.3 56.9 + - - +
209B GLY* 2.9 20.1 + - - -
210B TRP 3.9 12.7 - - - +
212B VAL* 3.7 20.9 + - + +
214B ARG* 2.8 44.0 + - - -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR 4.4 1.2 - - - +
199A ASP* 3.4 5.6 - - + -
200A ASP* 2.9 52.1 + - - +
203A MET* 3.6 11.4 - - + -
204A ARG* 3.5 24.2 - - + +
203B MET 2.9 12.1 + - - +
204B ARG 3.1 12.3 + - - +
206B GLU* 1.3 74.8 - - - +
208B TYR* 1.3 61.8 + - + +
209B GLY 3.2 0.8 + - - -
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 5.2 3.5 + - - -
199A ASP* 3.6 31.2 - - + +
204A ARG* 4.6 8.1 - - + -
208A TYR* 4.5 3.1 + - - -
164B HIS* 2.6 38.5 + + - +
167B CYS* 3.8 32.8 - - + +
168B SER* 3.8 11.3 - - - +
171B GLY* 3.1 26.5 - - - -
172B THR 4.4 0.3 + - - -
204B ARG* 2.9 59.1 + - + +
205B PHE* 3.0 22.9 + + - +
207B ALA* 1.3 77.2 - - + +
209B GLY* 1.3 56.8 + - - +
210B TRP* 3.5 10.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il